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Research Institute for Advanced Computer Science: Annual Report October 1998 through September 1999

The Research Institute for Advanced Computer Science (RIACS) carries out basic research and technology development in computer science, in support of the National Aeronautics and Space Administration's missions. RIACS is located at the NASA Ames Research Center (ARC). It currently operates under a multiple year grant/cooperative agreement that began on October 1, 1997 and is up for renewal in the year 2002. ARC has been designated NASA's Center of Excellence in Information Technology. In this capacity, ARC is charged with the responsibility to build an Information Technology Research Program that is preeminent within NASA. RIACS serves as a bridge between NASA ARC and the academic community, and RIACS scientists and visitors work in close collaboration with NASA scientists. RIACS has the additional goal of broadening the base of researchers in these areas of importance to the nation's space and aeronautics enterprises. RIACS research focuses on the three cornerstones of information technology research necessary to meet the future challenges of NASA missions: (1) Automated Reasoning for Autonomous Systems. Techniques are being developed enabling spacecraft that will be self-guiding and self-correcting to the extent that they will require little or no human intervention. Such craft will be equipped to independently solve problems as they arise, and fulfill their missions with minimum direction from Earth. (2) Human-Centered Computing. Many NASA missions require synergy between humans and computers, with sophisticated computational aids amplifying human cognitive and perceptual abilities; (3) High Performance Computing and Networking Advances in the performance of computing and networking continue to have major impact on a variety of NASA endeavors, ranging from modeling and simulation to data analysis of large datasets to collaborative engineering, planning and execution. In addition, RIACS collaborates with NASA scientists to apply information technology research to a variety of NASA application domains. RIACS also engages in other activities, such as workshops, seminars, and visiting scientist programs, designed to encourage and facilitate collaboration between the university and NASA information technology research communities.

Leiner, Barry M.↗

Research Institute for Advanced Computer Science

The Research Institute for Advanced Computer Science (RIACS) carries out basic research and technology development in computer science, in support of the National Aeronautics and Space Administration's missions. RIACS is located at the NASA Ames Research Center. It currently operates under a multiple year grant/cooperative agreement that began on October 1, 1997 and is up for renewal in the year 2002. Ames has been designated NASA's Center of Excellence in Information Technology. In this capacity, Ames is charged with the responsibility to build an Information Technology Research Program that is preeminent within NASA. RIACS serves as a bridge between NASA Ames and the academic community, and RIACS scientists and visitors work in close collaboration with NASA scientists. RIACS has the additional goal of broadening the base of researchers in these areas of importance to the nation's space and aeronautics enterprises. RIACS research focuses on the three cornerstones of information technology research necessary to meet the future challenges of NASA missions: (1) Automated Reasoning for Autonomous Systems. Techniques are being developed enabling spacecraft that will be self-guiding and self-correcting to the extent that they will require little or no human intervention. Such craft will be equipped to independently solve problems as they arise, and fulfill their missions with minimum direction from Earth; (2) Human-Centered Computing. Many NASA missions require synergy between humans and computers, with sophisticated computational aids amplifying human cognitive and perceptual abilities; (3) High Performance Computing and Networking. Advances in the performance of computing and networking continue to have major impact on a variety of NASA endeavors, ranging from modeling and simulation to data analysis of large datasets to collaborative engineering, planning and execution. In addition, RIACS collaborates with NASA scientists to apply information technology research to a variety of NASA application domains. RIACS also engages in other activities, such as workshops, seminars, and visiting scientist programs, designed to encourage and facilitate collaboration between the university and NASA information technology research communities.

Gross, Anthony R.↗

[Activities of Research Institute for Advanced Computer Science]

The Research Institute for Advanced Computer Science (RIACS) carries out basic research and technology development in computer science, in support of the National Aeronautics and Space Administrations missions. RIACS is located at the NASA Ames Research Center, Moffett Field, California. RIACS research focuses on the three cornerstones of IT research necessary to meet the future challenges of NASA missions: 1. Automated Reasoning for Autonomous Systems Techniques are being developed enabling spacecraft that will be self-guiding and self-correcting to the extent that they will require little or no human intervention. Such craft will be equipped to independently solve problems as they arise, and fulfill their missions with minimum direction from Earth. 2. Human-Centered Computing Many NASA missions require synergy between humans and computers, with sophisticated computational aids amplifying human cognitive and perceptual abilities. 3. High Performance Computing and Networking Advances in the performance of computing and networking continue to have major impact on a variety of NASA endeavors, ranging from modeling and simulation to analysis of large scientific datasets to collaborative engineering, planning and execution. In addition, RIACS collaborates with NASA scientists to apply IT research to a variety of NASA application domains. RIACS also engages in other activities, such as workshops, seminars, visiting scientist programs and student summer programs, designed to encourage and facilitate collaboration between the university and NASA IT research communities.

Gross, Anthony R.↗

IN13B-1660: Analytics and Visualization Pipelines for Big Data on the NASA Earth Exchange (NEX) and OpenNEX

We are developing capabilities for an integrated petabyte-scale Earth science collaborative analysis and visualization environment. The ultimate goal is to deploy this environment within the NASA Earth Exchange (NEX) and OpenNEX in order to enhance existing science data production pipelines in both high-performance computing (HPC) and cloud environments. Bridging of HPC and cloud is a fairly new concept under active research and this system significantly enhances the ability of the scientific community to accelerate analysis and visualization of Earth science data from NASA missions, model outputs and other sources. We have developed a web-based system that seamlessly interfaces with both high-performance computing (HPC) and cloud environments, providing tools that enable science teams to develop and deploy large-scale analysis, visualization and QA pipelines of both the production process and the data products, and enable sharing results with the community. Our project is developed in several stages each addressing separate challenge - workflow integration, parallel execution in either cloud or HPC environments and big-data analytics or visualization. This work benefits a number of existing and upcoming projects supported by NEX, such as the Web Enabled Landsat Data (WELD), where we are developing a new QA pipeline for the 25PB system.

visualization↗

QuakeSim and the Solid Earth Research Virtual Observatory

We are developing simulation and analysis tools in order to develop a solid Earth science framework for understanding and studying active tectonic and earthquake processes. The goal of QuakeSim and its extension, the Solid Earth Research Virtual Observatory (SERVO), is to study the physics of earthquakes using state-of-the-art modeling, data manipulation, and pattern recognition technologies. We are developing clearly defined accessible data formats and code protocols as inputs to simulations, which are adapted to high-performance computers. The solid Earth system is extremely complex and nonlinear resulting in computationally intensive problems with millions of unknowns. With these tools it will be possible to construct the more complex models and simulations necessary to develop hazard assessment systems critical for reducing future losses from major earthquakes. We are using Web (Grid) service technology to demonstrate the assimilation of multiple distributed data sources (a typical data grid problem) into a major parallel high-performance computing earthquake forecasting code. Such a linkage of Geoinformatics with Geocomplexity demonstrates the value of the Solid Earth Research Virtual Observatory (SERVO) Grid concept, and advances Grid technology by building the first real-time large-scale data assimilation grid.

virtual observatory↗

QRCODE: Massively parallelized real-time time-dependent density functional theory for periodic systems

We present a new software module, QRCODE (Quantum Research for Calculating Optically Driven Excitations), for massively parallelized real-time time-dependent density functional theory (RT-TDDFT) calculations of periodic systems in the open-source Qbox software package. Our approach utilizes a custom implementation of a fast Fourier transformation scheme that significantly reduces inter-node message passing interface (MPI) communication of the major computational kernel and shows impressive scaling up to 16,344 CPU cores. In addition to improving computational performance, QRCODE contains a suite of various time propagators for accurate RT-TDDFT calculations. As benchmark applications of QRCODE, we calculate the current density and optical absorption spectra of hexagonal boron nitride (h-BN) and photo-driven reaction dynamics of the ozone-oxygen reaction. We also calculate the second and higher harmonic generation of monolayer and multi-layer boron nitride structures as examples of large material systems. Our optimized implementation of RT-TDDFT in QRCODE enables large-scale calculations of real-time electron dynamics of chemical and material systems with enhanced computational performance and impressive scaling across several thousand CPU cores.

97 MATHEMATICS AND COMPUTING↗

Modeling Improvements and Users Manual for Axial-flow Turbine Off-design Computer Code AXOD

An axial-flow turbine off-design performance computer code used for preliminary studies of gas turbine systems was modified and calibrated based on the experimental performance of large aircraft-type turbines. The flow- and loss-model modifications and calibrations are presented in this report. Comparisons are made between computed performances and experimental data for seven turbines over wide ranges of speed and pressure ratio. This report also serves as the users manual for the revised code, which is named AXOD.

Glassman, Arthur J.↗

Application Table: A Bridge Connecting the Designing “With-The-Material” and “The-Material” Paradigms

Over the last few decades, advances in high-performance computing, new material characterization methods, and, more recently, an emphasis on integrated computational materials engineering (ICME) have been a catalyst for multiscale modeling and simulation-based design of materials and structures in the aerospace industry. In 2016 NASA sponsored a 2040 Vision study (which appeared in 2018) to define the potential 25-year future state required for integrated multiscale modeling of materials and systems (e.g., load-bearing structures) to accelerate the pace and reduce the expense of innovation in future aerospace and aeronautical systems. The study envisions a cyber-physical-social ecosystem comprised of experimentally verified and validated (V & V) computational models, tools, and techniques, along with the associated digital tapestry, that impacts the entire supply chain to enable cost-effective, rapid, and revolutionary design of “fit-for-purpose” materials, components, and systems. Consequently, the development of a robust information management system that incorporates (across the full life cycle) both experimental (real data) and virtual data resulting from the application of various simulation tools (at single or multiple length scales), therefore enabling the virtual design and optimization of materials throughout their processing – internal structure – property – performance envelope, has become critical. This need is also fueled by the demands for higher efficiency in material testing; consistency, quality, and traceability of data; product design; engineering analysis; as well as control of access to proprietary or sensitive information. This is particularly true when attempting to merge ICME practices with recent additive manufacturing technology which will enable production of the resulting 2040 Vision material and structural designs. At NASA Glenn Research Center we are exploring the future of material science through the use of novel characterization methodologies, high performance computing, and recently an emphasis on integrated computational materials engineering (ICME). Herein, recent efforts to incorporate an Application Table within NASA Glenn Research Center’s ICME Granta MI database is presented. The goal is to provide a place where material and structural application information/requirements can be linked so as to marry the “design the-material” and the “design-with-material” paradigms and thereby enable application-driven design and optimization of materials and structures by providing a central location that links material processing at various length scales to the application’s performance requirements. This paper discusses the specifics of this Application Table as well as best practices and key principles for the development of a robust materials information management system to enable the 2040 Vision integrated materials and structures ecosystem. Furthermore, it presents the intended role of the Application Table in the future of ICME design of “fit-for-purpose” materials, showing the need for a well-established framework that can successfully bridge the gap between the design “the material” and design “with-the-material” paradigms.

Materials↗

Application Table: A Bridge Connecting the Designing “With-the-Material” and “the-Material”

Over the last few decades, advances in high-performance computing, new material characterization methods, and, more recently, an emphasis on integrated computational materials engineering (ICME) have been a catalyst for multiscale modeling and simulation-based design of materials and structures in the aerospace industry. In 2016 NASA sponsored a 2040 Vision study (which appeared in 2018) to define the potential 25-year future state required for integrated multiscale modeling of materials and systems (e.g., load-bearing structures) to accelerate the pace and reduce the expense of innovation in future aerospace and aeronautical systems. The study envisions a cyber-physical-social ecosystem comprised of experimentally verified and validated (V & V) computational models, tools, and techniques, along with the associated digital tapestry, that impacts the entire supply chain to enable cost-effective, rapid, and revolutionary design of “fit-for-purpose” materials, components, and systems. Consequently, the development of a robust information management system that incorporates (across the full life cycle) both experimental (real data) and virtual data resulting from the application of various simulation tools (at single or multiple length scales), therefore enabling the virtual design and optimization of materials throughout their processing – internal structure – property – performance envelope, has become critical. This need is also fueled by the demands for higher efficiency in material testing; consistency, quality, and traceability of data; product design; engineering analysis; as well as control of access to proprietary or sensitive information. This is particularly true when attempting to merge ICME practices with recent additive manufacturing technology which will enable production of the resulting 2040 Vision material and structural designs. At NASA Glenn Research Center we are exploring the future of material science through the use of novel characterization methodologies, high performance computing, and recently an emphasis on integrated computational materials engineering (ICME). Herein, recent efforts to incorporate an Application Table within NASA Glenn Research Center’s ICME Granta MI database is presented. The goal is to provide a place where material and structural application information/requirements can be linked so as to marry the “design the-material” and the “design-with-material” paradigms and thereby enable application-driven design and optimization of materials and structures by providing a central location that links material processing at various length scales to the application’s performance requirements. This paper discusses the specifics of this Application Table as well as best practices and key principles for the development of a robust materials information management system to enable the 2040 Vision integrated materials and structures ecosystem. Furthermore, it presents the intended role of the Application Table in the future of ICME design of “fit-for-purpose” materials, showing the need for a well-established framework that can successfully bridge the gap between the design “the material” and design “with-the-material” paradigms.

Materials↗

ESnet-JLab FPGA Accelerated Transport (control plane) [EJFAT (udplbd2)] v2.0

The ESnet-JLab FPGA Accelerated Transport system is a solution for streaming high-speed scientific measurement data from Data Acquisition Systems (DAQs) to high-performance computing facilties. It is generally compatible with many science workflows, and makes no assumptions about the specifics of any particular experiment. This program (udplbd version 2) implements the control plane for the system. It is responsible for programming network forwarding rules into the data plane (implemented by the hardware designed named udplb, described separately). It also implements the control loop necessary to match up offered workload with available capacity on high-performance compute nodes.

Howard, Derek [Lawrence Berkeley National Laborato↗

Evaluation of Graph Analytics Frameworks Using the GAP Benchmark Suite

The analysis of connected data is an increasingly important application in high-performance computing. Such analyses can reveal fraudulent patterns in financial transactions, optimize telecommunications networks, predict information flow in social networks, etc. However, the landscape of graph analytics is highly diverse. Graph algorithms stress processor architectures differently, and no one graph can represent all topologies. Consequently, no single approach or framework is expected to be optimal for all graph analytics problems. To help make sense of this diverse landscape, we evaluated four approaches to graph analytics: GraphBLAS, Galois, BGL17, GraphIt; and compare them against hand-tuned implementations that take advantage of hardware features on our test platform. Graph- BLAS formulates graph analytics as sparse linear algebra. Galois provides syntactic constructs for data parallelism over irregular data structures. BGL17 is a generic C++ template library for implementing graph algorithms. GraphIt provides a domain- specific language to describe and optimize graph algorithms. We use the GAP Benchmark Suite to establish baseline performance and guide the side-by-side evaluation of each framework. GAP consists of 30 tests: six graph analytics algorithms (breadth- first search, single-source shortest path, PageRank, betweenness centrality, connected components, and triangle counting) run on five graphs, each with different topological characteristics (e.g., high diameter, skewed degree distribution, high average degree). High-performance reference implementations are included for each benchmark algorithm. Because a graph can be loaded into memory a number of ways (e.g., flat file on disk, compressed sparse format, data frames, retrieved from SQL or NoSQL databases), our evaluation focused on computational performance rather than I/O. Our results show the relative strengths of each framework.

Graph algorithms, Benchmarking, shared-memory prog↗

Oscillatory Spreading and Inertia in Power Grids

The increase in variable renewable generators (VRGs) in power systems has altered the dynamics from a historical experience. VRGs introduce new sources of power oscillations, and the stabilizing response provided by synchronous generators (SGs, e.g., natural gas, coal, etc.), which help avoid some power fluctuations, will lessen as VRGs replace SGs. These changes have led to the need for new methods and metrics to quickly assess the likely oscillatory behavior for a particular network without performing computationally expensive simulations. This work studies the impact of a critical dynamical parameter - the inertia value - on the rest of a power system's oscillatory response to representative VRG perturbations. We use a known localization metric in a novel way to quantify the number of nodes responding to a perturbation and the magnitude of those responses. This metric allows us to relate the spread and severity of a system's power oscillations with inertia. We find that as inertia increases, the system response to node perturbations transitions from localized (only a few close nodes respond) to delocalized (many nodes across the network respond). We introduce a heuristic computed from the network Laplacian to relate this oscillatory transition to the network structure. We show that our heuristic accurately describes the spread of oscillations for a realistic power-system test case. Using a heuristic to determine the likely oscillatory behavior of a system given a set of parameters has wide applicability in power systems, and it could decrease the computational workload of planning and operation.

dynamical systems↗

Numerical Propulsion System Simulation (NPSS) 1999 Industry Review

The technologies necessary to enable detailed numerical simulations of complete propulsion systems are being developed at the NASA Glenn Research Center in cooperation with industry, academia, and other government agencies. Large scale, detailed simulations will be of great value to the nation because they eliminate some of the costly testing required to develop and certify advanced propulsion systems. In addition, time and cost savings will be achieved by enabling design details to be evaluated early in the development process before a commitment is made to a specific design. This concept is called the Numerical Propulsion System Simulation (NPSS). NPSS consists of three main elements: (1) engineering models that enable multidisciplinary analysis of large subsystems and systems at various levels of detail, (2) a simulation environment that maximizes designer productivity, and (3) a cost-effective, high-performance computing platform. A fundamental requirement of the concept is that the simulations must be capable of overnight execution on easily accessible computing platforms. This will greatly facilitate the use of large-scale simulations in a design environment. This paper describes the current status of the NPSS with specific emphasis on the progress made over the past year on air breathing propulsion applications. In addition, the paper contains a summary of the feedback received from industry partners in the development effort and the actions taken over the past year to respond to that feedback. The NPSS development was supported in FY99 by the High Performance Computing and Communications Program.

Lytle, John↗

Validation of an In-Water, Tower-Shading Correction Scheme

Large offshore structures used for the deployment of optical instruments can significantly perturb the intensity of the light field surrounding the optical measurement point, where different portions of the visible spectrum are subject to different shadowing effects. These effects degrade the quality of the acquired optical data and can reduce the accuracy of several derived quantities, such as those obtained by applying bio-optical algorithms directly to the shadow-perturbed data. As a result, optical remote sensing calibration and validation studies can be impaired if shadowing artifacts are not fully accounted for. In this work, the general in-water shadowing problem is examined for a particular case study. Backward Monte Carlo (MC) radiative transfer computations- performed in a vertically stratified, horizontally inhomogeneous, and realistic ocean-atmosphere system are shown to accurately simulate the shadow-induced relative percent errors affecting the radiance and irradiance data profiles acquired close to an oceanographic tower. Multiparameter optical data processing has provided adequate representation of experimental uncertainties allowing consistent comparison with simulations. The more detailed simulations at the subsurface depth appear to be essentially equivalent to those obtained assuming a simplified ocean-atmosphere system, except in highly stratified waters. MC computations performed in the simplified system can be assumed, therefore, to accurately simulate the optical measurements conducted under more complex sampling conditions (i.e., within waters presenting moderate stratification at most). A previously reported correction scheme, based on the simplified MC simulations, and developed for subsurface shadow-removal processing of in-water optical data taken close to the investigated oceanographic tower, is then validated adequately under most experimental conditions. It appears feasible to generalize the present tower-specific approach to solve other optical sensor shadowing problems pertaining to differently shaped deployment platforms, and also including surrounding structures and instrument casings.

Hooker, Stanford B.↗

Implementation of Multispectral Image Classification on a Remote Adaptive Computer

As the demand for higher performance computers for the processing of remote sensing science algorithms increases, the need to investigate new computing paradigms its justified. Field Programmable Gate Arrays enable the implementation of algorithms at the hardware gate level, leading to orders of m a,gnitude performance increase over microprocessor based systems. The automatic classification of spaceborne multispectral images is an example of a computation intensive application, that, can benefit from implementation on an FPGA - based custom computing machine (adaptive or reconfigurable computer). A probabilistic neural network is used here to classify pixels of of a multispectral LANDSAT-2 image. The implementation described utilizes Java client/server application programs to access the adaptive computer from a remote site. Results verify that a remote hardware version of the algorithm (implemented on an adaptive computer) is significantly faster than a local software version of the same algorithm implemented on a typical general - purpose computer).

Figueiredo, Marco A.↗

Mixed-precision numerics in scientific applications: survey and perspectives

The explosive demand for artificial intelligence (AI) workloads has led to a significant increase in silicon area dedicated to lower-precision computations on recent high-performance computing hardware designs. However, mixed-precision capabilities, which can achieve performance improvements of up to 8x compared to double-precision in extreme compute-intensive workloads, remain largely untapped in most scientific applications. A growing number of efforts have shown that mixed-precision algorithmic innovations can deliver superior performance without sacrificing accuracy. These developments should prompt computational scientists to seriously consider whether their scientific modeling and simulation applications could benefit from the acceleration offered by new hardware and mixed-precision algorithms. In this survey, we (1) review progress across diverse scientific domains—fluid dynamics, weather and climate, quantum chemistry, and computational genomics—that have begun adopting mixed-precision strategies; (2) examine state-of-the-art algorithmic techniques such as iterative refinement, splitting and emulation schemes, and adaptive precision solvers; (3) assess their implications for accuracy, performance, and resource utilization; and (4) survey the emerging software ecosystem that enables mixed-precision methods at scale. We conclude with perspectives and recommendations on cross-cutting opportunities, domain-specific challenges, and the role of co-design between application scientists, numerical analysts, and computer scientists. Collectively, this survey underscores that mixed-precision numerics can reshape computational science by aligning algorithms with the evolving landscape of hardware capabilities.

Graphics processing units↗

Unstructured Grid Euler Method Assessment for Longitudinal and Lateral/Directional Aerodynamic Performance Analysis of the HSR Technology Concept Airplane at Supersonic Cruise Speed

Unstructured grid Euler computations, performed at supersonic cruise speed, are presented for a High Speed Civil Transport (HSCT) configuration, designated as the Technology Concept Airplane (TCA) within the High Speed Research (HSR) Program. The numerical results are obtained for the complete TCA cruise configuration which includes the wing, fuselage, empennage, diverters, and flow through nacelles at M (sub infinity) = 2.4 for a range of angles-of-attack and sideslip. Although all the present computations are performed for the complete TCA configuration, appropriate assumptions derived from the fundamental supersonic aerodynamic principles have been made to extract aerodynamic predictions to complement the experimental data obtained from a 1.675%-scaled truncated (aft fuselage/empennage components removed) TCA model. The validity of the computational results, derived from the latter assumptions, are thoroughly addressed and discussed in detail. The computed surface and off-surface flow characteristics are analyzed and the pressure coefficient contours on the wing lower surface are shown to correlate reasonably well with the available pressure sensitive paint results, particularly, for the complex flow structures around the nacelles. The predicted longitudinal and lateral/directional performance characteristics for the truncated TCA configuration are shown to correlate very well with the corresponding wind-tunnel data across the examined range of angles-of-attack and sideslip. The complementary computational results for the longitudinal and lateral/directional performance characteristics for the complete TCA configuration are also presented along with the aerodynamic effects due to empennage components. Results are also presented to assess the computational method performance, solution sensitivity to grid refinement, and solution convergence characteristics.

Ghaffari, Farhad↗

BMX: Biological modelling and interface exchange

Abstract High performance computing has a great potential to provide a range of significant benefits for investigating biological systems. These systems often present large modelling problems with many coupled subsystems, such as when studying colonies of bacteria cells. The aim to understand cell colonies has generated substantial interest as they can have strong economic and societal impacts through their roles in in industrial bioreactors and complex community structures, called biofilms, found in clinical settings. Investigating these communities through realistic models can rapidly exceed the capabilities of current serial software. Here, we introduce BMX, a software system developed for the high performance modelling of large cell communities by utilising GPU acceleration. BMX builds upon the AMRex adaptive mesh refinement package to efficiently model cell colony formation under realistic laboratory conditions. Using simple test scenarios with varying nutrient availability, we show that BMX is capable of correctly reproducing observed behavior of bacterial colonies on realistic time scales demonstrating a potential application of high performance computing to colony modelling. The open source software is available from the zenodo repository https://doi.org/10.5281/zenodo.8084270 under the BSD-2-Clause licence.

97 MATHEMATICS AND COMPUTING↗